Perhaps you could give a synopsis of it for those of us whose eyes glaze over when reading technical papers like this.
I’m no expert but I did take the holiday weekend to digest the paper and make some notes. Here is my synopsis, for what it is worth. Feel free to make corrections and additions.
Basics of cladistics
Organisms are classified according to a hierarchical system (taxonomy) first established by Carl Linnaeus. This system has traditionally been based on physical features, or morphology. With the advent of biotechnology there has been an ongoing effort to augment or replace morphology with DNA as the basis for taxonomy. These new approaches have taken on the name of cladistics. It is currently as much art as science but trending toward the latter.
This study examines the state of this art with respect to Roses and compares three different DNA technologies in an effort to decide which approach is best, while also giving useful taxonomies.
In all three methods DNA is processed with enzymes to create small fragments. The sequence of nucleic acids (the ‘genetic code’) are then compared using one of the three methods. For each of the three methods a taxonomy (phylogenetic tree) is given. These methods are:
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Unweighted Pair Group Method with Arithmetic mean, or UPGMA. This method yields a tree called a phenogram which is based essentially on similarities among the gene sequences. UPGMA is generally regarded as the least best method. The phenogram is given as figure 1.
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Parsimony. This method makes assumtions that the simplist (most parsimonius) evolutionary path is the correct one. From among many parsimony techniques the authors chose Wagner Parsimony to include in thier study, giving a number of reasons for this choice. Wagner Parsimony yields a “most parsimonious tree”, or MPT. In this study the authors actually made eight MPT’s, but published only one in their paper, which they said is actually the most parsimonious of the trees that they calculated. The MPT is given as figure 2.
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Bayesian Inference. This technique is based on complex algorithms that uses only Bayesian statistics (and so, no assumptions about the data) to generate a phylogenetic tree. The tree has no formal name, the authors simply call it “tree from the Bayesian analysis” and it is given as figure 3.
Each tree has a caption but the captions for each are presented two pages down from its respective tree, this being due to stylistic rules of publication for the American Journal of Botany. Thus, you will need to scroll about to view the caption for a given tree. It is annoying, but the captions are not so informative to us anyway.
The authors discuss differences among the three trees, but for our purposes they are pretty nearly the same. The authors believe that the Bayesian technique is probably best so use the third tree if you trust thier judgement.
For a general discussion on these methods see
It is also important to know that a given entry on a tree represents a single plant. Some species and some named hybrids are represented by more than one plant and so appear more than once on a tree. The major source of the plants used in this study was the Wageningen Botanical Garden, although some plants - especially hybrids - were obtained elsewhere from sources not identified.
How these trees help rose breeders
Probably the most important point from the study is this:
“Apparently, the cultivated gene pool [i.e. the various _hybrid_ roses used in the study] is relatively isolated from the wild gene pool [i.e. the true species roses]. This relatively isolated position is in line with the common practice of breeding new varieties by interbreeding of existing varieties, with only a limited use of wild germplasm. Our results show that the segregation of cultivated and wild accessions is not complete because several wild species cluster with the varieties. This incomplete segregation is also apparent in the results of Scariot et al. (2006) and may be a direct indication of a limited use of wild germplasm in the cultivated gene pool.”
Basically, some wild species have been used more than others and overall there is plenty of room left for breeders to incorporate species into the modern cultivars.
The species which have been used most often are those which cluster closely to the hybrid cultivars in the trees. The ones with the least contribution are those farthest away from the hybrids. This is no doubt old news to rose breeders but the trees do show which species contributed most to a given plant and so can help inform breeding strategies.
The trees can also help by application of the principle that the more closely related two individual plants are, the more likely that a cross can be successfully made.
The basic rule to use when interpreting the trees is the obvious one - the closer two plants are to each other the more closely related they are. The trees vary from each other slightly, but mostly they are very similar. The differences between trees are that one method may show one plant to be evolved from the other while another tree shows the two to be ‘sisters’ which have evolved from a common ancestor.
The authors mention, too, that in a number of instances there appear to be a ‘missing’ common ancestor, a relationship termed “polyphyletic” or “paraphyletic”. The major example cited is the subgroup Pimpinellifoliae, which (they claim) includes R.foetida, R. sericea, R. persica, R. roxburghii, R. hugonis and R. spinosissima, and they debate the pros and cons of lumping these in one group as opposed to splitting some out into separate subgenera. They explicitly say that R. persica (hulthemia) deserves to be demoted, and is not actually a subgenera as many taxonimists have previously claimed.
You will also see the term ‘clade’ used. “A clade is a taxonomic group (such as one of organisms) comprising a single common ancestor and all the descendants of that ancestor”(from wikipedia).
So roses with a polyphyletic relationship are by definition not a clade. But for purposes of informed breeding, and with the level of resolution these particular trees provide, such distinctions are essentially hair-splitting.
For a better explaination see
http://www.miketaylor.org.uk/dino/faq/s-class/phyletic/index.html
Hybridization muddies the water
You will notice that some plants, particularly R. multiflora, show up in several different places on the tree. This is because they sometimes used multiple different cultivars of that plant in thier study and these just happened to have genes different enough to fall out in different places on the tree. This should not be surprising especially for R. multiflora, given it’s wide use as a rootstock and it’s broad geographic distribution in nature which increases the likelihood that it has been hybridized, deliberately or not, and the genes which have mixed in cause the particular cultivar to fall closer to some modern ancestors than to the true wild type or species. One should not forget that rose breeding had been going on for over a thousand years in China before any of the Asian roses made it to western Europe.
Indeed, hybridization is mentioned by the authors as the big problem in establishing phylogenetic relationships in roses. At the same time, these trees do give clues about the dominant genetic contributions made in thier hybridization, and breeders can use these clues in planning thier breeding programs.
Unfortunately, and for no stated reason, two of the most important species of Rosa were not included in this study, R. Chinensis and R. Gigantea It is easy enough to guess why these were omitted. The authors are attempting to establish a baseline tree to be used for further study, and to allow discussion about which of the methods is best suited for the purpose. Some China roses, especially the teas, have been so heavily hybridized into modern cultivars that further work is going to be needed before the techniques have sufficient resolving power to discriminate among them. This is evidenced by the thicket assigned as “Rosa” on the trees, which includes most of the hybrid cultivars.
In addition to the generalizations above, there are some minor specifics in the paper that deserve attention.
You will come across mention of “satellite DNA” in several places in the study particularly in relation to the Canina group. It has recently been shown that R. canina has not only the usual complement of normal chromosomes in the nucleus, but also a group of DNA fragments that do not form a chromosome and which are present as a separate little cluster (during meiosis) in the nucleus. This group of DNA fragments is what is meant by satellite DNA. It seems so far to be unique to R. Canina and its offspring, and as can be imagined is a source of potential confusion to the taxonomists who have not so far figured out what it means or how it came about.
You will see the term ‘bootstrap’ in the study with respect to the first two trees and numbers at some branches on these two trees that are these bootstrap values. These have to do with the calculated validity of the branches presented.
In the Bayesian (third) tree there are numbers given at some branchs in the tree. These numbers are analagous to bootstrap values but represent the formal statistical probablility that the branch is real (and not an artifact of the method used). A probability index of 0.8 would therefore mean that there is about an 80% probability of the branch actually existing. Where no probability index is given, this means that the calculated probability was below some critical threshold and so is in relative doubt. You will notice a lot of branches that were detected but which have probabilities that are questionable. The authors are frank about this and much of the results section discusses the merit of particular branches.
The importance of these numbers is that the authors claim the Bayeseian probabilities are better than the bootstrapping values, and use this to support their contention that the Bayesian (third) tree is therefore best representative of the relationships among the roses tested.
You will note at the bottom of each tree there are three plants from the genus Rubus. These are the blackberry, European dewberry and the wineberry. They are included in the analysis as experimental controls. The idea is that because they are known to not be species of the genus Rosa they had better fall into their own genus in the computed results.
The authors discussed briefly, but rejected as immature, a method employing network analysis (as opposed to the three other methods used in this study). My personal opinion is that when this network methodology matures it may well become a very useful tool for breeders because it will allow us to have non-heirarchical, multi-dimensional maps that show the precise genetic relationship of every cultivar with respect to every other. In this way a tree becomes a network that represents not only evolutionary data but also hybridization relationships. Imagine the usefulness of map that allows the breeder to pick a cultivar and then see it’s nearest genetic neighbors, and thier nearest genetic neighbors, and so on. This is the likely direction that Bayesian techniques are heading toward.
